Tools

The FinnGen research project has developed a number of tools for the analysis, visualisation, and browsing of results, many of which are publicly available. FinnGen also shares the code for many of its analysis pipelines and the tools on its public GitHub site at https://github.com/FINNGEN/.

Risteys (Finnish word for a cross section) is a tool developed for FinnGen and FinRegistry projects and enables the investigation and browsing of the FinnGen endpoints. This can be done without applying for any special permissions.  

For browsing FinnGen core analysis GWAS association results FinnGen hosts several PheWebs.

Multiple Manhattan Plot is designed to explore GWAS results visually side by side. It can be used to compare any GWAS results. Common uses are meta-analyses of the same endpoint between different biobanks and comparisons between different endpoints.

The LAVAA volcano plot tool allows the viewing of the significance of PheWAS (phenome wide analysis results of a variant), and provides a quick view of the direction and magnitude of the effect across phenotypes. 

FinnGen Endpoint Browser is a tool for visualising hierarchy and relatedness between similar endpoints. It visualises how the endpoints are related in terms of ICD10 codes and patients' overlaps. 

Variant Cluster Corrector (V3C) is a graphical tool that can be used to improve the automatic genotype calls of the rare genetic variants and investigation of the batch variation of the genotypes.